Re: DCD File Not Generating

From: Ashkan Shekaari (
Date: Sat May 02 2020 - 05:30:42 CDT

Dear friend,
Clearly, the dcd frequency is tooooooo large.

All the best, 
Ashkan Shekaari, 
Ph.D Candidate in Solid State Physics, 
K. N. Toosi University of Technology, 
Tehran, Iran 
From: "Oscar Bastidas" <> 
To: "namd-l" <> 
Sent: Saturday, May 2, 2020 2:38:10 PM 
Subject: namd-l: DCD File Not Generating 
I am trying to run my simulations and my dcd files are never generated. I can't figure out why it's not working when this is something that has worked in the past for previous simulations/jobs. Furthermore, my cluster system indicates that the NAMD job terminated normally. 
The entire simulation is supposed to be several back to back simulations, but my first simulation never generates a dcd file. The log file even says that the coordinate dcd file was not created. 
Everything looks normal in my conf file as I've always had it for previous successful runs and I get no error files generated either. Could someone please offer me insight as to why no dcd file is ever being created? What could be causing this? 
I am using CHARMM-GUI to generate my simulation package. 
My conf file contents are below the line of asterisks. 
Oscar B. 
************************ ******** ******** ******** ******** ******** ******** 
structure step3_charmm2namd.psf 
coordinates step3_charmm2namd.pdb 
set temp 310.15; 
set outputname snapshot-1; 
#read system values written by CHARMM (need to convert uppercases to lowercases) 
exec tr "\[:upper:\]" "\[:lower:\]" < ../step3_pbcsetup.str | sed -e "s/ =//g" > step3_charmm2namd.str 
source step3_charmm2namd.str 
temperature $temp; 
outputName $outputname; 
firsttimestep 0; 
restartfreq 200000000; 
dcdfreq 200000000; 
dcdUnitCell yes; 
xstFreq 200000000; 
outputEnergies 200000000; 
outputTiming 200000000; 
paraTypeCharmm on; 
exclude scaled1-4 
1-4scaling 1.0 
switching on 
vdwForceSwitching yes; 
# You have some freedom choosing the cutoff 
cutoff 12.0; 
switchdist 10.0; 
pairlistdist 16.0; 
stepspercycle 20; 
pairlistsPerCycle 2; 
#Integrator Parameters 
timestep 2.0; 
rigidBonds all; 
nonbondedFreq 1; 
fullElectFrequency 1; 
# Constant Temperature Control ONLY DURING EQUILB 
reassignFreq 500; 
reassignTemp $temp; 
# Periodic Boundary conditions. Need this since for a start... 
cellBasisVector1 $a 0.0 0.0; 
cellBasisVector2 0.0 $b 0.0; 
cellBasisVector3 0.0 0.0 $c; 
cellOrigin 0.0 0.0 $zcen; 
wrapWater on; 
wrapAll on; 
wrapNearest off; 
# PME (for full-system periodic electrostatics) 
PME yes; 
PMEInterpOrder 6; 
PMEGridSpacing 1.0; 
# Pressure and volume control 
useGroupPressure yes; 
useFlexibleCell no; 
useConstantRatio no; 
langevin on 
langevinDamping 1.0 
langevinTemp $temp 
langevinHydrogen off 
# constant pressure 
langevinPiston on 
langevinPistonTarget 1.01325 
langevinPistonPeriod 50.0 
langevinPistonDecay 25.0 
langevinPistonTemp $temp 
# constraints on 
# consexp 2 
# consref restraints/prot_posres.ref 
# conskfile restraints/prot_posres.ref 
# conskcol B 
# constraintScaling 1.0 
minimize 10000 
# numsteps 90000000 
run 6250000; 

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